Casal2 Test Case MPD comparisons for LIN

1 LIN comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 6 Casal2 model configurations (3 BetaDiff and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-6 vs. 2e-3).

The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-6 vs. 2e-3).

1.1 LIN model characteristics

The main characteristics of the Test Case LIN (ling) CASAL model are:

• one stock, ages 3 - 25
• one area
• years 1972 - 2018, projection years 2019 - 2023
• two time steps: Dec_Aug and Sep_Nov
• two stock categories: male and female
• natural mortality-at-age is double exponential
• sex-specific maturity ogives specified by age
• sex-specific von Bertalanffy age-length relationship
• sex-specific length-weight relationship (\(W = aL^b\))
• Beverton-Holt stock-recruitment relationship, with steepness (h) 0.84
• ageing error
• two surveys with sex-specific logistic selectivity
• three fisheries, one with double normal selectivity and two with logistic selectivity

Observation data include:

• survey indices
• survey proportions-at-age
• fishery proportions-at-age

Parameters estimated include:

• B0
• parameters for the natural mortality-at-age ogive
• catchability (q) for the two surveys
• parameters for the sex-specific selectivity curves for the two surveys
• parameters for the sex-specific selectivity curves for the three fisheries
• YCS (recruitment deviations)

1.2 R environment

## [1] "Tue Nov 16 15:19:56 2021"
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux bookworm/sid
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.18.so
## 
## locale:
##  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8    
##  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8   
##  [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] Casal2_21.10   casal_2.30     devtools_2.4.2 usethis_2.1.3  rlist_0.4.6.2 
##  [6] ggthemes_4.2.4 gridExtra_2.3  coda_0.19-4    ggmcmc_1.5.1.1 ggplot2_3.3.5 
## [11] tidyr_1.1.4    huxtable_5.4.0 dplyr_1.0.7    plyr_1.8.6    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7         lattice_0.20-45    prettyunits_1.1.1  ps_1.6.0          
##  [5] assertthat_0.2.1   rprojroot_2.0.2    digest_0.6.28      utf8_1.2.2        
##  [9] R6_2.5.1           evaluate_0.14      pillar_1.6.4       rlang_0.4.12      
## [13] data.table_1.14.2  callr_3.7.0        jquerylib_0.1.4    rmarkdown_2.11    
## [17] desc_1.4.0         stringr_1.4.0      munsell_0.5.0      compiler_4.1.2    
## [21] xfun_0.28          pkgconfig_2.0.3    pkgbuild_1.2.0     htmltools_0.5.2   
## [25] tidyselect_1.1.1   tibble_3.1.6       reshape_0.8.8      fansi_0.5.0       
## [29] crayon_1.4.2       withr_2.4.2        grid_4.1.2         jsonlite_1.7.2    
## [33] GGally_2.1.2       gtable_0.3.0       lifecycle_1.0.1    DBI_1.1.1         
## [37] magrittr_2.0.1     scales_1.1.1       cli_3.1.0          stringi_1.7.5     
## [41] cachem_1.0.6       fs_1.5.0           remotes_2.4.1      testthat_3.1.0    
## [45] bslib_0.3.1        ellipsis_0.3.2     generics_0.1.1     vctrs_0.3.8       
## [49] RColorBrewer_1.1-2 tools_4.1.2        glue_1.5.0         purrr_0.3.4       
## [53] processx_3.5.2     pkgload_1.2.3      fastmap_1.1.0      yaml_2.2.1        
## [57] colorspace_2.0-2   sessioninfo_1.2.1  memoise_2.0.0      knitr_1.36        
## [61] sass_0.4.0

1.3 CASAL and Casal2 model output

source('../../R-functions/report_read_in_CASAL_MPD_files.R')

source('../../R-functions/report_read_in_Casal2_MPD_files.R')

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates

rownames	Base_Model	Sensitivity_1	Percent_Diff
q[tan_sum].q	0.09128	0.09105	0.252
q[tan_aut].q	0.12620	0.12590	0.238
initialization.B0	309000.00000	310700.00000	-0.550
natural_mortality.ogive_all1	12.49000	12.98000	-3.923
natural_mortality.ogive_all2	0.13270	0.12780	3.693
natural_mortality.ogive_all3	0.38190	0.44990	-17.806
natural_mortality.ogive_all4	0.35060	0.35390	-0.941
selectivity[surveysum_sel].male1	4.73800	4.88100	-3.018
selectivity[surveysum_sel].male2	1.75000	1.77200	-1.257
selectivity[surveysum_sel].male3	0.61000	0.60160	1.377
selectivity[surveysum_sel].female1	5.46000	5.61300	-2.802
selectivity[surveysum_sel].female2	2.20600	2.21500	-0.408
selectivity[surveyaut_sel].male1	5.50400	5.64400	-2.544
selectivity[surveyaut_sel].male2	2.31400	2.29800	0.691
selectivity[surveyaut_sel].male3	0.93920	0.93310	0.649
selectivity[surveyaut_sel].female1	5.92000	6.06200	-2.399
selectivity[surveyaut_sel].female2	2.77800	2.73800	1.440
selectivity[trawl_sel].male1	8.37000	8.40400	-0.406
selectivity[trawl_sel].male2	1.97200	1.94700	1.268
selectivity[trawl_sel].male3	61.65000	200.00000	-224.412
selectivity[trawl_sel].male4	1.04100	1.02100	1.921
selectivity[trawl_sel].female1	8.66400	8.74100	-0.889
selectivity[trawl_sel].female2	2.10000	2.08800	0.571
selectivity[trawl_sel].female3	43.31000	40.38000	6.765
selectivity[line_home_sel].male1	11.45000	8.58300	25.039
selectivity[line_home_sel].male2	8.59000	4.54700	47.066
selectivity[line_home_sel].male3	0.38010	0.26910	29.203
selectivity[line_home_sel].female1	9.61600	9.53100	0.884
selectivity[line_home_sel].female2	3.87500	3.68500	4.903
selectivity[line_spawn_sel].male1	18.30000	14.04000	23.279
selectivity[line_spawn_sel].male2	13.67000	10.01000	26.774
selectivity[line_spawn_sel].male3	1.86800	1.17300	37.206
selectivity[line_spawn_sel].female1	9.74600	9.71300	0.339
selectivity[line_spawn_sel].female2	3.00800	2.89400	3.790
recruitment.YCS1	1.00000	1.00000	0.000
recruitment.YCS2	1.00000	1.00000	0.000
recruitment.YCS3	1.00000	1.00000	0.000
recruitment.YCS4	1.00000	1.00000	0.000
recruitment.YCS5	0.48500	0.46620	3.876
recruitment.YCS6	0.45830	0.45010	1.789
recruitment.YCS7	0.56860	0.56470	0.686
recruitment.YCS8	0.56670	0.56670	0.000
recruitment.YCS9	0.48610	0.49070	-0.946
recruitment.YCS10	0.55500	0.56720	-2.198
recruitment.YCS11	0.56320	0.57880	-2.770
recruitment.YCS12	0.68760	0.71090	-3.389
recruitment.YCS13	0.62030	0.63610	-2.547
recruitment.YCS14	0.79060	0.80840	-2.251
recruitment.YCS15	0.46430	0.46930	-1.077
recruitment.YCS16	0.70080	0.70730	-0.928
recruitment.YCS17	0.41010	0.41050	-0.098
recruitment.YCS18	0.51500	0.51450	0.097
recruitment.YCS19	0.34160	0.34220	-0.176
recruitment.YCS20	0.34830	0.34730	0.287
recruitment.YCS21	0.43610	0.43820	-0.482
recruitment.YCS22	0.48060	0.47500	1.165
recruitment.YCS23	0.45220	0.45130	0.199
recruitment.YCS24	0.49170	0.49480	-0.630
recruitment.YCS25	0.46910	0.47070	-0.341
recruitment.YCS26	0.79930	0.80490	-0.701
recruitment.YCS27	0.79010	0.79210	-0.253
recruitment.YCS28	0.82610	0.83110	-0.605
recruitment.YCS29	0.70760	0.71250	-0.692
recruitment.YCS30	0.55170	0.55430	-0.471
recruitment.YCS31	0.47520	0.47680	-0.337
recruitment.YCS32	0.46170	0.46140	0.065
recruitment.YCS33	0.55500	0.55430	0.126
recruitment.YCS34	0.54670	0.54210	0.841
recruitment.YCS35	0.48320	0.48250	0.145
recruitment.YCS36	0.55020	0.54990	0.055
recruitment.YCS37	0.61530	0.61580	-0.081
recruitment.YCS38	0.77570	0.77470	0.129
recruitment.YCS39	0.63110	0.63060	0.079
recruitment.YCS40	0.77550	0.77350	0.258
recruitment.YCS41	0.64290	0.63930	0.560
recruitment.YCS42	0.70670	0.69940	1.033
recruitment.YCS43	0.65430	0.64860	0.871
recruitment.YCS44	0.51000	0.50620	0.745
recruitment.YCS45	0.58620	0.58730	-0.188
recruitment.YCS46	0.60350	0.58930	2.353
recruitment.YCS47	0.57680	0.57450	0.399

Casal2 parameter estimates

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	308529.00000	308529.00000	310577.00000	308529.00000	308529.00000	310577.00000
catchability[summerTANq].q	0.09137	0.09137	0.09106	0.09137	0.09137	0.09106
catchability[autumnTANq].q	0.12607	0.12607	0.12594	0.12607	0.12607	0.12594
selectivity[M_all].x0	12.49650	12.49650	12.98440	12.49650	12.49650	12.98440
selectivity[M_all].y0	0.13262	0.13262	0.12797	0.13262	0.13262	0.12797
selectivity[M_all].y1	0.38280	0.38280	0.44726	0.38280	0.38280	0.44726
selectivity[M_all].y2	0.35113	0.35113	0.35373	0.35113	0.35113	0.35373
selectivity[summerTANSel_m].a50	4.73988	4.73988	4.87645	4.73988	4.73988	4.87645
selectivity[summerTANSel_m].ato95	1.74459	1.74459	1.77029	1.74459	1.74459	1.77029
selectivity[summerTANSel_m].alpha	0.60995	0.60995	0.60184	0.60995	0.60995	0.60184
selectivity[summerTANSel_f].a50	5.46111	5.46111	5.60807	5.46111	5.46111	5.60807
selectivity[summerTANSel_f].ato95	2.20340	2.20340	2.21420	2.20340	2.20340	2.21420
selectivity[autumnTANSel_m].a50	5.50982	5.50982	5.63972	5.50982	5.50982	5.63972
selectivity[autumnTANSel_m].ato95	2.31271	2.31271	2.29781	2.31271	2.31271	2.29781
selectivity[autumnTANSel_m].alpha	0.94173	0.94173	0.93320	0.94173	0.94173	0.93320
selectivity[autumnTANSel_f].a50	5.91574	5.91574	6.05848	5.91574	5.91574	6.05848
selectivity[autumnTANSel_f].ato95	2.77020	2.77020	2.73846	2.77020	2.77020	2.73846
selectivity[trwlFSel_m].mu	8.36919	8.36919	8.40239	8.36919	8.36919	8.40239
selectivity[trwlFSel_m].sigma_l	1.97023	1.97023	1.94735	1.97023	1.97023	1.94735
selectivity[trwlFSel_m].sigma_r	61.52290	61.52290	200.00000	61.52290	61.52290	200.00000
selectivity[trwlFSel_m].alpha	1.04276	1.04276	1.02085	1.04276	1.04276	1.02085
selectivity[trwlFSel_f].mu	8.65854	8.65854	8.73949	8.65854	8.65854	8.73949
selectivity[trwlFSel_f].sigma_l	2.09656	2.09656	2.08849	2.09656	2.09656	2.08849
selectivity[trwlFSel_f].sigma_r	43.16390	43.16390	40.59470	43.16390	43.16390	40.59470
selectivity[lineHomeFSel_m].a50	11.45600	11.45600	8.60835	11.45600	11.45600	8.60835
selectivity[lineHomeFSel_m].ato95	8.59958	8.59958	4.59169	8.59958	8.59958	4.59169
selectivity[lineHomeFSel_m].alpha	0.38022	0.38022	0.26993	0.38022	0.38022	0.26993
selectivity[lineHomeFSel_f].a50	9.61476	9.61476	9.53352	9.61476	9.61476	9.53352
selectivity[lineHomeFSel_f].ato95	3.87014	3.87014	3.69064	3.87014	3.87014	3.69064
selectivity[lineSpawnFSel_m].a50	18.21510	18.21510	14.04670	18.21510	18.21510	14.04670
selectivity[lineSpawnFSel_m].ato95	13.59950	13.59950	10.02610	13.59950	13.59950	10.02610
selectivity[lineSpawnFSel_m].alpha	1.85634	1.85634	1.17449	1.85634	1.85634	1.17449
selectivity[lineSpawnFSel_f].a50	9.73862	9.73862	9.71478	9.73862	9.73862	9.71478
selectivity[lineSpawnFSel_f].ato95	2.99387	2.99387	2.89670	2.99387	2.99387	2.89670
process[Recruitment].ycs_values{1972}	0.48379	0.48379	0.46642	0.48379	0.48379	0.46642
process[Recruitment].ycs_values{1973}	0.46122	0.46122	0.45020	0.46122	0.46122	0.45020
process[Recruitment].ycs_values{1974}	0.56837	0.56837	0.56454	0.56837	0.56837	0.56454
process[Recruitment].ycs_values{1975}	0.56652	0.56652	0.56688	0.56652	0.56652	0.56688
process[Recruitment].ycs_values{1976}	0.48635	0.48635	0.49081	0.48635	0.48635	0.49081
process[Recruitment].ycs_values{1977}	0.55413	0.55413	0.56717	0.55413	0.55413	0.56717
process[Recruitment].ycs_values{1978}	0.56316	0.56316	0.57855	0.56316	0.56316	0.57855
process[Recruitment].ycs_values{1979}	0.68899	0.68899	0.71094	0.68899	0.68899	0.71094
process[Recruitment].ycs_values{1980}	0.62093	0.62093	0.63619	0.62093	0.62093	0.63619
process[Recruitment].ycs_values{1981}	0.79247	0.79247	0.80802	0.79247	0.79247	0.80802
process[Recruitment].ycs_values{1982}	0.46507	0.46507	0.46929	0.46507	0.46507	0.46929
process[Recruitment].ycs_values{1983}	0.69967	0.69967	0.70706	0.69967	0.69967	0.70706
process[Recruitment].ycs_values{1984}	0.40995	0.40995	0.41042	0.40995	0.40995	0.41042
process[Recruitment].ycs_values{1985}	0.51540	0.51540	0.51456	0.51540	0.51540	0.51456
process[Recruitment].ycs_values{1986}	0.34131	0.34131	0.34212	0.34131	0.34131	0.34212
process[Recruitment].ycs_values{1987}	0.34760	0.34760	0.34728	0.34760	0.34760	0.34728
process[Recruitment].ycs_values{1988}	0.43791	0.43791	0.43826	0.43791	0.43791	0.43826
process[Recruitment].ycs_values{1989}	0.47924	0.47924	0.47501	0.47924	0.47924	0.47501
process[Recruitment].ycs_values{1990}	0.45181	0.45181	0.45133	0.45181	0.45181	0.45133
process[Recruitment].ycs_values{1991}	0.49264	0.49264	0.49479	0.49264	0.49264	0.49479
process[Recruitment].ycs_values{1992}	0.46918	0.46918	0.47070	0.46918	0.46918	0.47070
process[Recruitment].ycs_values{1993}	0.79791	0.79791	0.80486	0.79791	0.79791	0.80486
process[Recruitment].ycs_values{1994}	0.79128	0.79128	0.79208	0.79128	0.79128	0.79208
process[Recruitment].ycs_values{1995}	0.82538	0.82538	0.83109	0.82538	0.82538	0.83109
process[Recruitment].ycs_values{1996}	0.70728	0.70728	0.71249	0.70728	0.70728	0.71249
process[Recruitment].ycs_values{1997}	0.55206	0.55206	0.55427	0.55206	0.55206	0.55427
process[Recruitment].ycs_values{1998}	0.47508	0.47508	0.47683	0.47508	0.47508	0.47683
process[Recruitment].ycs_values{1999}	0.46119	0.46119	0.46140	0.46119	0.46119	0.46140
process[Recruitment].ycs_values{2000}	0.55575	0.55575	0.55442	0.55575	0.55575	0.55442
process[Recruitment].ycs_values{2001}	0.54546	0.54546	0.54206	0.54546	0.54546	0.54206
process[Recruitment].ycs_values{2002}	0.48373	0.48373	0.48263	0.48373	0.48373	0.48263
process[Recruitment].ycs_values{2003}	0.54989	0.54989	0.54993	0.54989	0.54989	0.54993
process[Recruitment].ycs_values{2004}	0.61418	0.61418	0.61578	0.61418	0.61418	0.61578
process[Recruitment].ycs_values{2005}	0.77712	0.77712	0.77462	0.77712	0.77712	0.77462
process[Recruitment].ycs_values{2006}	0.63130	0.63130	0.63052	0.63130	0.63130	0.63052
process[Recruitment].ycs_values{2007}	0.77377	0.77377	0.77345	0.77377	0.77377	0.77345
process[Recruitment].ycs_values{2008}	0.64251	0.64251	0.63928	0.64251	0.64251	0.63928
process[Recruitment].ycs_values{2009}	0.70649	0.70649	0.69935	0.70649	0.70649	0.69935
process[Recruitment].ycs_values{2010}	0.65312	0.65312	0.64871	0.65312	0.65312	0.64871
process[Recruitment].ycs_values{2011}	0.51136	0.51136	0.50623	0.51136	0.51136	0.50623
process[Recruitment].ycs_values{2012}	0.58556	0.58556	0.58738	0.58556	0.58556	0.58738
process[Recruitment].ycs_values{2013}	0.60064	0.60064	0.58912	0.60064	0.60064	0.58912
process[Recruitment].ycs_values{2014}	0.57601	0.57601	0.57450	0.57601	0.57601	0.57450

Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	0.000	0.000	-0.664	0.000	0.000	-0.664
catchability[summerTANq].q	0.000	0.000	0.344	0.000	0.000	0.344
catchability[autumnTANq].q	0.000	0.000	0.105	0.000	0.000	0.105
selectivity[M_all].x0	0.000	0.000	-3.904	0.000	0.000	-3.904
selectivity[M_all].y0	0.000	0.000	3.510	0.000	0.000	3.510
selectivity[M_all].y1	0.000	0.000	-16.840	0.000	0.000	-16.840
selectivity[M_all].y2	0.000	0.000	-0.741	0.000	0.000	-0.741
selectivity[summerTANSel_m].a50	0.000	0.000	-2.881	0.000	0.000	-2.881
selectivity[summerTANSel_m].ato95	0.000	0.000	-1.473	0.000	0.000	-1.473
selectivity[summerTANSel_m].alpha	0.000	0.000	1.329	0.000	0.000	1.329
selectivity[summerTANSel_f].a50	0.000	0.000	-2.691	0.000	0.000	-2.691
selectivity[summerTANSel_f].ato95	0.000	0.000	-0.490	0.000	0.000	-0.490
selectivity[autumnTANSel_m].a50	0.000	0.000	-2.358	0.000	0.000	-2.358
selectivity[autumnTANSel_m].ato95	0.000	0.000	0.644	0.000	0.000	0.644
selectivity[autumnTANSel_m].alpha	0.000	0.000	0.906	0.000	0.000	0.906
selectivity[autumnTANSel_f].a50	0.000	0.000	-2.413	0.000	0.000	-2.413
selectivity[autumnTANSel_f].ato95	0.000	0.000	1.146	0.000	0.000	1.146
selectivity[trwlFSel_m].mu	0.000	0.000	-0.397	0.000	0.000	-0.397
selectivity[trwlFSel_m].sigma_l	0.000	0.000	1.161	0.000	0.000	1.161
selectivity[trwlFSel_m].sigma_r	0.000	0.000	-225.082	0.000	0.000	-225.082
selectivity[trwlFSel_m].alpha	0.000	0.000	2.101	0.000	0.000	2.101
selectivity[trwlFSel_f].mu	0.000	0.000	-0.935	0.000	0.000	-0.935
selectivity[trwlFSel_f].sigma_l	0.000	0.000	0.385	0.000	0.000	0.385
selectivity[trwlFSel_f].sigma_r	0.000	0.000	5.952	0.000	0.000	5.952
selectivity[lineHomeFSel_m].a50	0.000	0.000	24.857	0.000	0.000	24.857
selectivity[lineHomeFSel_m].ato95	0.000	0.000	46.606	0.000	0.000	46.606
selectivity[lineHomeFSel_m].alpha	0.000	0.000	29.007	0.000	0.000	29.007
selectivity[lineHomeFSel_f].a50	0.000	0.000	0.845	0.000	0.000	0.845
selectivity[lineHomeFSel_f].ato95	0.000	0.000	4.638	0.000	0.000	4.638
selectivity[lineSpawnFSel_m].a50	0.000	0.000	22.884	0.000	0.000	22.884
selectivity[lineSpawnFSel_m].ato95	0.000	0.000	26.276	0.000	0.000	26.276
selectivity[lineSpawnFSel_m].alpha	0.000	0.000	36.731	0.000	0.000	36.731
selectivity[lineSpawnFSel_f].a50	0.000	0.000	0.245	0.000	0.000	0.245
selectivity[lineSpawnFSel_f].ato95	0.000	0.000	3.246	0.000	0.000	3.246
process[Recruitment].ycs_values{1972}	0.000	0.000	3.589	0.000	0.000	3.589
process[Recruitment].ycs_values{1973}	0.000	0.000	2.389	0.000	0.000	2.389
process[Recruitment].ycs_values{1974}	0.000	0.000	0.675	0.000	0.000	0.675
process[Recruitment].ycs_values{1975}	0.000	0.000	-0.064	0.000	0.000	-0.064
process[Recruitment].ycs_values{1976}	0.000	0.000	-0.916	0.000	0.000	-0.916
process[Recruitment].ycs_values{1977}	0.000	0.000	-2.353	0.000	0.000	-2.353
process[Recruitment].ycs_values{1978}	0.000	0.000	-2.733	0.000	0.000	-2.733
process[Recruitment].ycs_values{1979}	0.000	0.000	-3.185	0.000	0.000	-3.185
process[Recruitment].ycs_values{1980}	0.000	0.000	-2.457	0.000	0.000	-2.457
process[Recruitment].ycs_values{1981}	0.000	0.000	-1.962	0.000	0.000	-1.962
process[Recruitment].ycs_values{1982}	0.000	0.000	-0.906	0.000	0.000	-0.906
process[Recruitment].ycs_values{1983}	0.000	0.000	-1.056	0.000	0.000	-1.056
process[Recruitment].ycs_values{1984}	0.000	0.000	-0.115	0.000	0.000	-0.115
process[Recruitment].ycs_values{1985}	0.000	0.000	0.162	0.000	0.000	0.162
process[Recruitment].ycs_values{1986}	0.000	0.000	-0.236	0.000	0.000	-0.236
process[Recruitment].ycs_values{1987}	0.000	0.000	0.091	0.000	0.000	0.091
process[Recruitment].ycs_values{1988}	0.000	0.000	-0.079	0.000	0.000	-0.079
process[Recruitment].ycs_values{1989}	0.000	0.000	0.884	0.000	0.000	0.884
process[Recruitment].ycs_values{1990}	0.000	0.000	0.106	0.000	0.000	0.106
process[Recruitment].ycs_values{1991}	0.000	0.000	-0.436	0.000	0.000	-0.436
process[Recruitment].ycs_values{1992}	0.000	0.000	-0.325	0.000	0.000	-0.325
process[Recruitment].ycs_values{1993}	0.000	0.000	-0.871	0.000	0.000	-0.871
process[Recruitment].ycs_values{1994}	0.000	0.000	-0.102	0.000	0.000	-0.102
process[Recruitment].ycs_values{1995}	0.000	0.000	-0.691	0.000	0.000	-0.691
process[Recruitment].ycs_values{1996}	0.000	0.000	-0.736	0.000	0.000	-0.736
process[Recruitment].ycs_values{1997}	0.000	0.000	-0.400	0.000	0.000	-0.400
process[Recruitment].ycs_values{1998}	0.000	0.000	-0.368	0.000	0.000	-0.368
process[Recruitment].ycs_values{1999}	0.000	0.000	-0.045	0.000	0.000	-0.045
process[Recruitment].ycs_values{2000}	0.000	0.000	0.239	0.000	0.000	0.239
process[Recruitment].ycs_values{2001}	0.000	0.000	0.623	0.000	0.000	0.623
process[Recruitment].ycs_values{2002}	0.000	0.000	0.227	0.000	0.000	0.227
process[Recruitment].ycs_values{2003}	0.000	0.000	-0.008	0.000	0.000	-0.008
process[Recruitment].ycs_values{2004}	0.000	0.000	-0.260	0.000	0.000	-0.260
process[Recruitment].ycs_values{2005}	0.000	0.000	0.321	0.000	0.000	0.321
process[Recruitment].ycs_values{2006}	0.000	0.000	0.123	0.000	0.000	0.123
process[Recruitment].ycs_values{2007}	0.000	0.000	0.042	0.000	0.000	0.042
process[Recruitment].ycs_values{2008}	0.000	0.000	0.503	0.000	0.000	0.503
process[Recruitment].ycs_values{2009}	0.000	0.000	1.010	0.000	0.000	1.010
process[Recruitment].ycs_values{2010}	0.000	0.000	0.674	0.000	0.000	0.674
process[Recruitment].ycs_values{2011}	0.000	0.000	1.004	0.000	0.000	1.004
process[Recruitment].ycs_values{2012}	0.000	0.000	-0.311	0.000	0.000	-0.311
process[Recruitment].ycs_values{2013}	0.000	0.000	1.918	0.000	0.000	1.918
process[Recruitment].ycs_values{2014}	0.000	0.000	0.262	0.000	0.000	0.262

CASAL objective function component values

Component	Base_Model	Sensitivity_1
Tangaroa_bio_autumn	-6.829	-6.834
Tangaroa_bio_summer	-23.880	-23.960
Tangaroa_propn_at_age_aut	175.700	175.800
Tangaroa_propn_at_age_summer	835.900	835.600
longline_Campbell_home_propn_at_age	275.700	275.400
longline_Puysegur_spawn_propn_at_age	363.300	363.300
trawl_observer_propn_at_age	682.600	682.300
prior_on_q[tan_sum].q	-2.364	-2.366
prior_on_q[tan_aut].q	-2.033	-2.037
prior_on_initialization.B0	12.640	12.650
prior_on_natural_mortality.ogive_all	0.000	0.000
prior_on_selectivity[surveysum_sel].male	0.000	0.000
prior_on_selectivity[surveysum_sel].female	0.000	0.000
prior_on_selectivity[surveyaut_sel].male	0.000	0.000
prior_on_selectivity[surveyaut_sel].female	0.000	0.000
prior_on_selectivity[trawl_sel].male	0.000	0.000
prior_on_selectivity[trawl_sel].female	0.000	0.000
prior_on_selectivity[line_home_sel].male	0.000	0.000
prior_on_selectivity[line_home_sel].female	0.000	0.000
prior_on_selectivity[line_spawn_sel].male	0.000	0.000
prior_on_selectivity[line_spawn_sel].female	0.000	0.000
prior_on_recruitment.YCS	-14.440	-14.370
clp1	0.000	0.000
clp2	0.000	0.000
clp3	0.000	0.000
YCS_average_1	0.908	0.903
Total	2297.000	2296.000

Casal2 objective function component values

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
observation->summerTANbiomass-1992	-1.693	-1.693	-1.679	-1.693	-1.693	-1.679
observation->summerTANbiomass-1993	-1.353	-1.353	-1.331	-1.353	-1.353	-1.331
observation->summerTANbiomass-1994	-0.975	-0.975	-0.991	-0.975	-0.975	-0.991
observation->summerTANbiomass-2001	0.430	0.430	0.354	0.430	0.430	0.354
observation->summerTANbiomass-2002	-1.778	-1.778	-1.786	-1.778	-1.778	-1.786
observation->summerTANbiomass-2003	-1.685	-1.685	-1.693	-1.685	-1.685	-1.693
observation->summerTANbiomass-2004	-1.598	-1.598	-1.586	-1.598	-1.598	-1.586
observation->summerTANbiomass-2005	-1.657	-1.657	-1.656	-1.657	-1.657	-1.656
observation->summerTANbiomass-2006	-1.143	-1.143	-1.153	-1.143	-1.143	-1.153
observation->summerTANbiomass-2007	-1.162	-1.162	-1.180	-1.162	-1.162	-1.180
observation->summerTANbiomass-2008	-1.568	-1.568	-1.553	-1.568	-1.568	-1.553
observation->summerTANbiomass-2009	-1.700	-1.700	-1.705	-1.700	-1.700	-1.705
observation->summerTANbiomass-2010	-1.672	-1.672	-1.678	-1.672	-1.672	-1.678
observation->summerTANbiomass-2012	-1.554	-1.554	-1.558	-1.554	-1.554	-1.558
observation->summerTANbiomass-2013	-1.669	-1.669	-1.667	-1.669	-1.669	-1.667
observation->summerTANbiomass-2015	-1.582	-1.582	-1.570	-1.582	-1.582	-1.570
observation->summerTANbiomass-2017	-1.526	-1.526	-1.528	-1.526	-1.526	-1.528
observation->Tangaroa_propn_at_age_summer-1990	44.218	44.218	44.393	44.218	44.218	44.393
observation->Tangaroa_propn_at_age_summer-1992	51.993	51.993	51.753	51.993	51.993	51.753
observation->Tangaroa_propn_at_age_summer-1993	50.200	50.200	50.168	50.200	50.200	50.168
observation->Tangaroa_propn_at_age_summer-1994	49.743	49.743	49.785	49.743	49.743	49.785
observation->Tangaroa_propn_at_age_summer-2001	48.355	48.355	48.237	48.355	48.355	48.237
observation->Tangaroa_propn_at_age_summer-2002	47.830	47.830	47.879	47.830	47.830	47.879
observation->Tangaroa_propn_at_age_summer-2003	48.442	48.442	48.620	48.442	48.442	48.620
observation->Tangaroa_propn_at_age_summer-2004	44.823	44.823	44.865	44.823	44.823	44.865
observation->Tangaroa_propn_at_age_summer-2005	43.097	43.097	43.117	43.097	43.097	43.117
observation->Tangaroa_propn_at_age_summer-2006	43.891	43.891	44.058	43.891	43.891	44.058
observation->Tangaroa_propn_at_age_summer-2007	41.848	41.848	41.841	41.848	41.848	41.841
observation->Tangaroa_propn_at_age_summer-2008	45.225	45.225	45.266	45.225	45.225	45.266
observation->Tangaroa_propn_at_age_summer-2009	46.844	46.844	46.806	46.844	46.844	46.806
observation->Tangaroa_propn_at_age_summer-2010	47.128	47.128	47.202	47.128	47.128	47.202
observation->Tangaroa_propn_at_age_summer-2012	44.353	44.353	44.183	44.353	44.353	44.183
observation->Tangaroa_propn_at_age_summer-2013	47.251	47.251	47.021	47.251	47.251	47.021
observation->Tangaroa_propn_at_age_summer-2015	46.473	46.473	46.342	46.473	46.473	46.342
observation->Tangaroa_propn_at_age_summer-2017	44.182	44.182	44.082	44.182	44.182	44.082
observation->autumnTANbiomass-1992	-1.558	-1.558	-1.572	-1.558	-1.558	-1.572
observation->autumnTANbiomass-1993	-1.741	-1.741	-1.733	-1.741	-1.741	-1.733
observation->autumnTANbiomass-1996	-1.779	-1.779	-1.779	-1.779	-1.779	-1.779
observation->autumnTANbiomass-1998	-1.750	-1.750	-1.750	-1.750	-1.750	-1.750
observation->Tangaroa_propn_at_age_autumn-1992	44.589	44.589	44.443	44.589	44.589	44.443
observation->Tangaroa_propn_at_age_autumn-1993	45.484	45.484	45.443	45.484	45.484	45.443
observation->Tangaroa_propn_at_age_autumn-1996	42.184	42.184	42.295	42.184	42.184	42.295
observation->Tangaroa_propn_at_age_autumn-1998	43.464	43.464	43.610	43.464	43.464	43.610
observation->trawl_propn_at_age-1992	36.067	36.067	35.944	36.067	36.067	35.944
observation->trawl_propn_at_age-1993	27.516	27.516	27.476	27.516	27.516	27.476
observation->trawl_propn_at_age-1994	25.819	25.819	25.764	25.819	25.819	25.764
observation->trawl_propn_at_age-1996	28.394	28.394	28.397	28.394	28.394	28.397
observation->trawl_propn_at_age-1998	24.915	24.915	24.910	24.915	24.915	24.910
observation->trawl_propn_at_age-2001	24.580	24.580	24.542	24.580	24.580	24.542
observation->trawl_propn_at_age-2002	26.770	26.770	26.792	26.770	26.770	26.792
observation->trawl_propn_at_age-2003	34.564	34.564	34.511	34.564	34.564	34.511
observation->trawl_propn_at_age-2004	29.608	29.608	29.608	29.608	29.608	29.608
observation->trawl_propn_at_age-2005	30.147	30.147	30.166	30.147	30.147	30.166
observation->trawl_propn_at_age-2006	33.629	33.629	33.714	33.629	33.629	33.714
observation->trawl_propn_at_age-2007	26.635	26.635	26.588	26.635	26.635	26.588
observation->trawl_propn_at_age-2008	27.059	27.059	27.076	27.059	27.059	27.076
observation->trawl_propn_at_age-2009	37.213	37.213	37.237	37.213	37.213	37.237
observation->trawl_propn_at_age-2010	30.648	30.648	30.694	30.648	30.648	30.694
observation->trawl_propn_at_age-2011	31.266	31.266	31.260	31.266	31.266	31.260
observation->trawl_propn_at_age-2012	32.325	32.325	32.366	32.325	32.325	32.366
observation->trawl_propn_at_age-2013	37.072	37.072	36.943	37.072	37.072	36.943
observation->trawl_propn_at_age-2014	30.640	30.640	30.642	30.640	30.640	30.642
observation->trawl_propn_at_age-2015	33.456	33.456	33.474	33.456	33.456	33.474
observation->trawl_propn_at_age-2016	36.532	36.532	36.482	36.532	36.532	36.482
observation->trawl_propn_at_age-2017	37.755	37.755	37.708	37.755	37.755	37.708
observation->longline_Campbell_home_propn_at_age-1999	45.348	45.348	45.256	45.348	45.348	45.256
observation->longline_Campbell_home_propn_at_age-2001	31.965	31.965	31.950	31.965	31.965	31.950
observation->longline_Campbell_home_propn_at_age-2003	28.644	28.644	28.675	28.644	28.644	28.675
observation->longline_Campbell_home_propn_at_age-2005	32.750	32.750	32.776	32.750	32.750	32.776
observation->longline_Campbell_home_propn_at_age-2009	26.033	26.033	25.611	26.033	26.033	25.611
observation->longline_Campbell_home_propn_at_age-2010	24.302	24.302	24.461	24.302	24.302	24.461
observation->longline_Campbell_home_propn_at_age-2011	28.878	28.878	28.935	28.878	28.878	28.935
observation->longline_Campbell_home_propn_at_age-2012	32.258	32.258	32.388	32.258	32.258	32.388
observation->longline_Campbell_home_propn_at_age-2014	25.495	25.495	25.357	25.495	25.495	25.357
observation->longline_Puyseger_home_propn_at_age-2000	42.745	42.745	42.680	42.745	42.745	42.680
observation->longline_Puyseger_home_propn_at_age-2001	31.770	31.770	31.900	31.770	31.770	31.900
observation->longline_Puyseger_home_propn_at_age-2002	39.978	39.978	39.998	39.978	39.978	39.998
observation->longline_Puyseger_home_propn_at_age-2003	43.527	43.527	43.511	43.527	43.527	43.511
observation->longline_Puyseger_home_propn_at_age-2004	39.957	39.957	40.015	39.957	39.957	40.015
observation->longline_Puyseger_home_propn_at_age-2005	25.532	25.532	25.358	25.532	25.532	25.358
observation->longline_Puyseger_home_propn_at_age-2006	35.210	35.210	35.426	35.210	35.210	35.426
observation->longline_Puyseger_home_propn_at_age-2007	33.981	33.981	33.782	33.981	33.981	33.782
observation->longline_Puyseger_home_propn_at_age-2008	19.139	19.139	19.113	19.139	19.139	19.113
observation->longline_Puyseger_home_propn_at_age-2010	24.238	24.238	24.366	24.238	24.238	24.366
observation->longline_Puyseger_home_propn_at_age-2017	27.200	27.200	27.093	27.200	27.200	27.093
prior->B0->process[Recruitment].b0	12.640	12.640	12.646	12.640	12.640	12.646
prior->summerTANq->catchability[summerTANq].q	-2.363	-2.363	-2.365	-2.363	-2.363	-2.365
prior->autumnTANq->catchability[autumnTANq].q	-2.035	-2.035	-2.037	-2.035	-2.035	-2.037
prior->M_all_x0->selectivity[M_all].x0	0.000	0.000	0.000	0.000	0.000	0.000
prior->M_all_y0->selectivity[M_all].y0	0.000	0.000	0.000	0.000	0.000	0.000
prior->M_all_y1->selectivity[M_all].y1	0.000	0.000	0.000	0.000	0.000	0.000
prior->M_all_y2->selectivity[M_all].y2	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_m].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_m].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_f].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_f].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_m].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_m].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_f].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_f].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_m].mu	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_m].sigma_l	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_m].sigma_r	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_f].mu	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_f].sigma_l	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_f].sigma_r	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_m].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_m].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_f].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_f].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_m].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_m].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_f].a50	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_f].ato95	0.000	0.000	0.000	0.000	0.000	0.000
prior->process[Recruitment].ycs_values{1972}	-0.378	-0.378	-0.365	-0.378	-0.378	-0.365
prior->process[Recruitment].ycs_values{1973}	-0.360	-0.360	-0.349	-0.360	-0.360	-0.349
prior->process[Recruitment].ycs_values{1974}	-0.397	-0.397	-0.398	-0.397	-0.397	-0.398
prior->process[Recruitment].ycs_values{1975}	-0.398	-0.398	-0.398	-0.398	-0.398	-0.398
prior->process[Recruitment].ycs_values{1976}	-0.380	-0.380	-0.383	-0.380	-0.380	-0.383
prior->process[Recruitment].ycs_values{1977}	-0.399	-0.399	-0.398	-0.399	-0.399	-0.398
prior->process[Recruitment].ycs_values{1978}	-0.398	-0.398	-0.396	-0.398	-0.398	-0.396
prior->process[Recruitment].ycs_values{1979}	-0.335	-0.335	-0.316	-0.335	-0.335	-0.316
prior->process[Recruitment].ycs_values{1980}	-0.380	-0.380	-0.372	-0.380	-0.380	-0.372
prior->process[Recruitment].ycs_values{1981}	-0.231	-0.231	-0.213	-0.231	-0.231	-0.213
prior->process[Recruitment].ycs_values{1982}	-0.364	-0.364	-0.367	-0.364	-0.364	-0.367
prior->process[Recruitment].ycs_values{1983}	-0.326	-0.326	-0.319	-0.326	-0.326	-0.319
prior->process[Recruitment].ycs_values{1984}	-0.291	-0.291	-0.292	-0.291	-0.291	-0.292
prior->process[Recruitment].ycs_values{1985}	-0.394	-0.394	-0.393	-0.394	-0.394	-0.393
prior->process[Recruitment].ycs_values{1986}	-0.114	-0.114	-0.117	-0.114	-0.114	-0.117
prior->process[Recruitment].ycs_values{1987}	-0.135	-0.135	-0.134	-0.135	-0.135	-0.134
prior->process[Recruitment].ycs_values{1988}	-0.334	-0.334	-0.334	-0.334	-0.334	-0.334
prior->process[Recruitment].ycs_values{1989}	-0.375	-0.375	-0.372	-0.375	-0.375	-0.372
prior->process[Recruitment].ycs_values{1990}	-0.350	-0.350	-0.350	-0.350	-0.350	-0.350
prior->process[Recruitment].ycs_values{1991}	-0.384	-0.384	-0.385	-0.384	-0.384	-0.385
prior->process[Recruitment].ycs_values{1992}	-0.367	-0.367	-0.369	-0.367	-0.367	-0.369
prior->process[Recruitment].ycs_values{1993}	-0.225	-0.225	-0.217	-0.225	-0.225	-0.217
prior->process[Recruitment].ycs_values{1994}	-0.233	-0.233	-0.232	-0.233	-0.233	-0.232
prior->process[Recruitment].ycs_values{1995}	-0.192	-0.192	-0.185	-0.192	-0.192	-0.185
prior->process[Recruitment].ycs_values{1996}	-0.319	-0.319	-0.315	-0.319	-0.319	-0.315
prior->process[Recruitment].ycs_values{1997}	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399
prior->process[Recruitment].ycs_values{1998}	-0.372	-0.372	-0.373	-0.372	-0.372	-0.373
prior->process[Recruitment].ycs_values{1999}	-0.360	-0.360	-0.360	-0.360	-0.360	-0.360
prior->process[Recruitment].ycs_values{2000}	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399
prior->process[Recruitment].ycs_values{2001}	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399
prior->process[Recruitment].ycs_values{2002}	-0.378	-0.378	-0.377	-0.378	-0.378	-0.377
prior->process[Recruitment].ycs_values{2003}	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399
prior->process[Recruitment].ycs_values{2004}	-0.383	-0.383	-0.383	-0.383	-0.383	-0.383
prior->process[Recruitment].ycs_values{2005}	-0.249	-0.249	-0.251	-0.249	-0.249	-0.251
prior->process[Recruitment].ycs_values{2006}	-0.375	-0.375	-0.375	-0.375	-0.375	-0.375
prior->process[Recruitment].ycs_values{2007}	-0.252	-0.252	-0.253	-0.252	-0.252	-0.253
prior->process[Recruitment].ycs_values{2008}	-0.368	-0.368	-0.370	-0.368	-0.368	-0.370
prior->process[Recruitment].ycs_values{2009}	-0.320	-0.320	-0.326	-0.320	-0.320	-0.326
prior->process[Recruitment].ycs_values{2010}	-0.362	-0.362	-0.364	-0.362	-0.362	-0.364
prior->process[Recruitment].ycs_values{2011}	-0.392	-0.392	-0.390	-0.392	-0.392	-0.390
prior->process[Recruitment].ycs_values{2012}	-0.394	-0.394	-0.393	-0.394	-0.394	-0.393
prior->process[Recruitment].ycs_values{2013}	-0.389	-0.389	-0.393	-0.389	-0.389	-0.393
prior->process[Recruitment].ycs_values{2014}	-0.396	-0.396	-0.396	-0.396	-0.396	-0.396
additional_prior->YCS_average_1	0.908	0.908	0.904	0.908	0.908	0.904
total_score	2296.970	2296.970	2296.140	2296.970	2296.970	2296.140

## [1] "CASAL base model convergence information"
## [1] "fmm: have converged: t = 0.00198541 f = 2297.19"                                                        
## [2] "Successful convergence in optimise"                                                                     
## [3] "Minimiser achieved convergence after 53 quasi-Newton iterations using 91 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-006"                                                                  
## [2] "fmm: have converged: t = 4.30035e-007 f = 2296.34"                                                        
## [3] "Successful convergence in optimise"                                                                       
## [4] "Minimiser achieved convergence after 188 quasi-Newton iterations using 303 objective function evaluations"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: have converged: t = 4.70876e-07 f = 2296.14"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## character(0)

## [1] "CASAL model warnings"
## NULL
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
##                        parameter estimate lower.bound upper.bound
## 1 selectivity[trawl_sel].male[3]      200           1         200
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## [2] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## [2] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others…

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.7359 0.9329"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.9871 0.9823"

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.762745 0.93218"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.762745 0.93218"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.989428 0.979127"

## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.762745 0.93218"

## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.762745 0.93218"

## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.989428 0.979127"